Replacing a body control module because you got them to respray some panels sounds like a scam to me. Unless spraypaint got into it, there is no reason it would break. And even then, they would be at fault, because it was working perfectly when you came in, you said.
If they insist and you can't get them to repair it at their cost, i'd let another garage do the repair. (also gets you some form of second opinion) If that's not possible and they have to do it, at least ask for them to give the old body control module to you when they're done. That way they can't get money off of taking parts of your car and selling them on Ebay. They may charge you for taking the old part, but that's pure BS. It's not even legal in my country. I'd resist if they ask that.
I know i sound exceptionally suspicious, but believe me these kind of situations are not unusual. Running a garage alone doesn't make you very rich, so there's many unfair mechanics that try to bump their income a bit this way. No offense to the fair and honest mechanics here though.